All the JFK hotels are dumps, except the TWA and the brand new Hyatt Regency JFK, which costs 12k Hyatt points (which you can buy until Sept 30 for 200 USD; cash rates are $350+). You would need a $20 Uber to the Hyatt each way, but they come very fast. I always stay there using my Hyatt cat. 1-4 certificates.The thread for the new Hyatt Regency JFK is here:

Hyatt Regency JFK Airport at Resorts World New York - REVIEW MASTER THREAD

Other than that, I would rather go to some new Courtyards around LGA that at least they will be less likely to have bedbugs....

PS. I always search the tripadvisor hotel reviews for bedbugs, and this really narrows down the field, lol...